cytotoxic T cell differentiation / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class I protein binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling / T cell receptor signaling pathway / defense response to virus ...cytotoxic T cell differentiation / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class I protein binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling / T cell receptor signaling pathway / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / receptor complex / external side of plasma membrane / protein kinase binding / cell surface / identical protein binding / plasma membrane Similarity search - Function
Monochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97945 Å / Relative weight: 1
Reflection
Av σ(I) over netI: 9.6 / Number: 147032 / Rmerge(I) obs: 0.131 / Χ2: 1.04 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 44334 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
5.81
50
91.7
1
0.062
0.967
4.62
5.81
94.1
1
0.102
1.072
4.03
4.62
94.9
1
0.121
1.078
3.66
4.03
96.7
1
0.16
1.028
3.4
3.66
99
1
0.196
1
3.2
3.4
99.8
1
0.201
0.978
3.04
3.2
99.9
1
0.251
1.061
2.91
3.04
99.8
1
0.324
1.056
2.8
2.91
99.9
1
0.427
1.083
2.7
2.8
99.8
1
0.579
1.078
Reflection
Resolution: 2.7→50 Å / Num. obs: 45395 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.04 / Net I/σ(I): 9.6
Reflection shell
Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.17 / Num. unique all: 4468 / Χ2: 1.078 / % possible all: 99.8
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
REFMAC
refinement
PDB_EXTRACT
3.004
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.33 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 32.285 / SU ML: 0.327 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.22 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.284
2216
5 %
RANDOM
Rwork
0.235
-
-
-
obs
0.238
42077
97.57 %
-
all
-
42077
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 55.349 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.44 Å2
0 Å2
0 Å2
2-
-
2.26 Å2
0 Å2
3-
-
-
1.17 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→42.33 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10234
0
28
36
10298
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
10500
X-RAY DIFFRACTION
r_bond_other_d
0.007
0.02
7042
X-RAY DIFFRACTION
r_angle_refined_deg
1.576
1.957
14262
X-RAY DIFFRACTION
r_angle_other_deg
0.907
3.002
17238
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.612
5
1316
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.958
24.417
412
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.508
15
1768
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.609
15
40
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
1626
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
11534
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2058
X-RAY DIFFRACTION
r_nbd_refined
0.238
0.2
1903
X-RAY DIFFRACTION
r_nbd_other
0.215
0.2
6879
X-RAY DIFFRACTION
r_nbtor_refined
0.188
0.2
4915
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
5890
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.172
0.2
255
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.083
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.312
0.2
19
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.277
0.2
47
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.244
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
2.452
3
8295
X-RAY DIFFRACTION
r_mcbond_other
0.324
3
2656
X-RAY DIFFRACTION
r_mcangle_it
2.847
5
10730
X-RAY DIFFRACTION
r_scbond_it
5.145
8
4653
X-RAY DIFFRACTION
r_scangle_it
6.595
11
3532
Refine LS restraints NCS
Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
L
1232
LOOSEPOSITIONAL
0.34
5
2
L
1182
LOOSEPOSITIONAL
0.41
5
3
H
1400
LOOSEPOSITIONAL
0.37
5
4
H
1069
LOOSEPOSITIONAL
0.4
5
5
C
1381
LOOSEPOSITIONAL
0.49
5
6
F
1340
LOOSEPOSITIONAL
0.4
5
1
L
1232
LOOSETHERMAL
2.19
10
2
L
1182
LOOSETHERMAL
3.09
10
3
H
1400
LOOSETHERMAL
2.33
10
4
H
1069
LOOSETHERMAL
3.48
10
5
C
1381
LOOSETHERMAL
2
10
6
F
1340
LOOSETHERMAL
2.2
10
LS refinement shell
Resolution: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.409
176
-
Rwork
0.35
3110
-
all
-
3286
-
obs
-
-
99.76 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.047
-0.158
-0.1148
2.3459
-1.3918
3.7626
-0.0641
0.1236
-0.2313
-0.0954
0.1119
0.1992
0.185
-0.0949
-0.0478
0.0436
-0.0537
0.0256
-0.2441
-0.0368
-0.1367
-11.457
-52.993
28.988
2
3.7105
-1.3326
-1.1487
2.8598
0.1486
4.2374
0.0189
0.0748
0.2389
0.0694
-0.0448
-0.0833
-0.3646
-0.0258
0.0259
0.1454
-0.0606
-0.0434
-0.179
0.0246
-0.1106
-10.893
-31.577
22.646
3
5.2663
1.0535
-1.5055
7.3194
-0.1706
3.5586
0.1363
-0.5768
-0.1706
1.8856
-0.2249
0.9634
-0.1394
0.128
0.0886
0.4023
-0.0933
0.327
-0.6488
0.0556
-0.142
-24.77
-31.203
57.438
4
3.6763
-3.4059
-1.4777
9.7319
1.6069
4.3508
0.0091
0.0265
-0.0652
0.5449
0.2888
2.2957
0.0067
-0.3773
-0.2979
0.0298
-0.113
0.3965
-0.7258
0.0654
0.524
-35.822
-41.374
53.551
5
2.9065
0.2779
-0.4172
2.9795
-1.82
4.5673
-0.0378
0.0716
-0.105
-0.0562
-0.0122
0.0896
0.2621
0.0149
0.05
0.04
-0.027
0.0343
-0.3486
-0.0589
-0.188
-11.574
-99.067
43.431
6
7.7354
-3.4514
-2.5049
10.0169
2.9611
1.4374
-0.4197
-0.1947
-0.1464
1.6106
0.6861
2.2848
-0.4335
-0.6874
-0.2664
0.4413
0.2939
0.5748
-0.2132
0.3422
0.3543
-36.817
-89.716
67.272
7
0.8145
-0.0568
-1.5649
4.0813
0.1708
4.4951
0.1635
0.0144
0.1612
0.2156
0.0381
0.0749
-0.3888
-0.0256
-0.2016
0.0866
-0.0102
0.0429
-0.2327
0.0277
-0.074
-11.183
-77.485
37.897
8
8.1254
-2.3329
0.2196
12.4945
-8.8831
17.5056
-0.6291
-1.1141
0.3608
3.3012
0.9273
-0.3995
-1.6252
0.1229
-0.2983
1.1369
0.4372
0.1779
-0.3599
-0.1631
-0.0221
-26.653
-78.678
72.163
9
8.9485
-1.7767
-1.8237
3.6503
1.0932
5.6359
0.166
0.9206
-0.6294
-0.0664
-0.1756
0.2895
0.1987
0.0377
0.0096
-0.2476
0.0221
0.0262
-0.053
-0.0634
-0.2797
15.777
-95.217
5.47
10
6.9845
-0.4207
-1.2056
4.3443
1.0365
4.8589
0.0437
0.6617
-0.7042
0.0213
-0.2563
0.2572
0.3271
-0.0237
0.2127
-0.2584
-0.006
0.0327
0.0135
-0.0908
-0.296
15.768
-50.32
-9.373
11
3.463
0.6504
0.6124
2.1955
0.4226
2.4565
-0.1372
0.5288
0.2586
-0.1433
0.0543
-0.0315
-0.1897
0.1635
0.0829
-0.0816
-0.0113
0.0832
0.0179
0.0225
-0.183
-2.792
-84.855
11.902
12
3.6786
0.16
0.555
2.039
0.455
4.2916
-0.0083
0.6705
0.2767
-0.2049
-0.0372
-0.0261
-0.2429
0.3204
0.0455
-0.0845
-0.0141
0.0558
0.0048
0.0381
-0.2449
-2.677
-39.873
-3.038
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
L
1 - 109
2
X-RAY DIFFRACTION
2
H
1 - 110
3
X-RAY DIFFRACTION
3
H
121 - 210
4
X-RAY DIFFRACTION
4
L
110 - 210
5
X-RAY DIFFRACTION
5
D
1 - 109
6
X-RAY DIFFRACTION
6
D
110 - 210
7
X-RAY DIFFRACTION
7
B
1 - 110
8
X-RAY DIFFRACTION
8
B
121 - 210
9
X-RAY DIFFRACTION
9
A
4 - 110
10
X-RAY DIFFRACTION
10
C
4 - 110
11
X-RAY DIFFRACTION
11
E
4 - 110
12
X-RAY DIFFRACTION
12
R
1 - 110
+
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